Phenotypic and genetic variability of a tetraploid wheat collection grown in Kazakhstan

New cultivars adapted to major durum wheat growing environments are essential for the cultivation of this crop. The development of new cultivars has required the availability of diverse genetic material and their extensive field trials. In this work, a collection of tetraploid wheat consisting of 85 accessions was tested in the field conditions of Almaty region during 2018 and 2019. The accessions were ranged according to nine agronomic traits studied, and accessions with the highest yield performance for Almaty region of Kazakhstan were revealed. The ANOVA suggested that the performance of agronomic traits were influenced both by Environment and Genotype. Also, the collection was analyzed using seven SSR (simple sequence repeats) markers. From 3 to 6 alleles per locus were revealed, with an average of 4.6, while the effective number of alleles was 2.8. Nei’s genetic diversity was in the range of 0.45–0.69. The results showed high values of polymorphism index content (PIC) in the range of 0.46–0.70, with an average of 0.62, suggesting that 6 out of 7 SSRs were highly informative (PIC > 0.5). Phylogenetic analysis of the collection has allowed the separation of accessions into six clusters. The local accessions were presented in all six clusters with the majority of them grouped in the first three clusters designated as A, B, and C, respectively. The relations between SSR markers and agronomic traits in the collection were studied. The results can be efficiently used for the enhancement of local breeding projects for the improvement of yield productivity in durum wheat

GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases

Soybean (Glycine max (L.) Merr) is an essential food, feed, and technical culture. In Kazakhstan the area under soybean is increasing every year, helping to solve the problem of protein deficiency in human nutrition and animal feeding. One of the main problems of soybean production is fungal diseases causing yields losses of up to 30 %. Modern genomic studies can be applied to facilitate efficient breeding research for improvement of soybean fungal disease tolerance. Therefore, the objective of this genome-wide association study (GWAS) was analysis of a soybean collection consisting of 182 accessions in relation to fungal diseases in the conditions of South East and South Kazakh­stan. Field evaluation of the soybean collection suggested that Fusarium spp. and Cercospora sojina affected plants in the South region (RIBSP), and Septoria glycines – in the South East region (KRIAPP). The major objective of the study was identification of QTL associated with resistance to fusarium root rot (FUS), frogeye leaf spot (FLS), and brown spot (BS). GWAS using 4 442 SNP (single nucleotide polymorphism) markers of Illumina iSelect array allowed for identification of fifteen marker trait associations (MTA) resistant to the three diseases at two different stages of growth. Two QTL both for FUS (chromosomes 13 and 17) and BS (chromosomes 14 and 17) were genetically mapped, including one presumably novel QTL for BS (chromo­some 17). Also, five presumably novel QTL for FLS were genetically mapped on chromosomes 2, 7, and 15. The results can be used for improvement of the local breeding projects based on marker-assisted selection approach

Conspectus of the genus <i>Juniperus</i> L. growing in Kazakhstan

Background. The genus Juniperus L. is the most numerous in the family Cupressaceae Bartl. and includes about 75 species. There are from 7 to 10 species of this genus in Kazakhstan. All types of juniper are widely used in folk medicine and play an important ecological role. The purpose of our work was to study the current status, systematics and distribution of juniper species. This will help to clarify and expand the information on the current location of Juniperus species in Kazakhstan and will be used in the future to study intra- and interspecific genetic diversity of the genus.Materials and methods. To study the distribution and make a conspectus of the Juniperus spp. growing in Kazakhstan, floristic reports, materials of plant explorations and the herbarium collections for the period from 1890 to 2021 obtained from the herbarium of the Institute of Botany and Phytointroduction (AA), herbarium materials of the Institute of Plant Biology and Biotechnology as well as the digital herbarium of the Lomonosov Moscow State University – Depository of Living Systems “Noah’s Ark” (MW) were analyzed.Results. As a result of the study, 630 herbarium sheets were processed and 70 locations of 7 juniper species growing in Kazakhstan belonging to 2 sections – Juniperus (=Oxycedrus Endl.) and Sabina Endl. – were identified. A conspectus of 7 juniper species identified during the analysis of the three above-mentioned herbarium collections was made. The main division of species is observed in the context of administrative and floristic regions of Kazakhstan. The greatest species concentration occurs in Southern, South-Eastern and Eastern Kazakhstan. The results of the study contribute to the inventory and search for previously forgotten places of growth for the genus Juniperus. Besides, the continuation of comprehensive botanical and molecular genetic studies on junipers will help to examine and preserve the genetic diversity of the species and conserve forest bioresources

A study of the genetic diversity in the world soybean collection using microsatellite markers associated with fungal disease resistance

Background. Soybean (Glycine max (L.) Merr.) gradually becomes one of the leading legume crops in Kazakhstan. The area under soybeans in the country has been increasing annually and requires the development of adapted cultivars with a higher yield, improved quality characters, and resistance to emerging fungal diseases. The enlargement of the crop’s gene pool also suggests the need to study and document local soybean accessions to meet the standards of the available world soybean collection by using reliable and informative types of DNA markers.Materials and methods. In this study, the soybean collection consisting of 288 accessions from different countries, including 36 cultivars and promising lines from Kazakhstan, was studied. The molecular genetic analysis was performed using nine polymorphic SSR (simple sequence repeats) markers, seven of which (Satt244, Satt565, Satt038, Satt309, Satt371, Satt570 and Sat_308) were associated with resistance to three main fungal diseases of soybean – frogeye leaf spot, fusarium root rot, and purple seed stain.Results. The average PIC (polymorphism information content) value of the analyzed SSR markers constituted 0.66 ± 0.07, confirming their highlevel polymorphism. The principal coordinate analysis suggested that the local accessions were genetically most close to the accessions from East Asia. As the collection showed a robust resistance to three studied fungal diseases in Almaty Region during 2018–2019, the distribution of the studied SSR markers in the population was not significantly associated with resistance to the analyzed diseases under field conditions.Conclusion. SSR genotyping of the soybean collection helped to identify accessions that potentially possess resistance-associated alleles of fungal disease resistance genes. The data obtained can be further used for the development of DNA documentation and the breeding the promising cultivars and lines of soybean

SSR-based evaluation of genetic diversity in populations of Agriophyllum squarrosum L. and Agriophyllum minus Fisch. & Mey. collected in South-East Kazakhstan

The development of informative polymorphic DNA markers for poorly studied genera is an important step in population analyses of living organisms, including those that play very important ecological roles in harsh environments, such as desert and semi-desert area. Examples of those poorly studied desert species are Agriophyllum squarrosum L. and Agriophyllum minus Fisch. &amp; Mey. However, a recent RNA-sequencing project in A. squarrosum has proposed a large set of hypothetical SSR (simple sequence repeat) markers. In this work, 11 novel polymorphic SSRs were found due to the screening of 24 randomly selected SSRs for three populations of A. squarrosum and one population of A. minus. The analysis of 11 SSRs revealed 16 polymorphic loci in two Agriophyllum species, 8 polymorphic loci within three populations of A. squarrosum, and 6 polymorphic loci in the population of A. minus. Statistical analyses showed high interspecific, but relatively low intraspecific genetic diversity. The phylogenetic clusterization and population structure analysis have demonstrated a clear segregation of A. minus from A. squarrosum, as well as the separation of population 1 from populations 2 and 3 of A. squarrosum. Thus, we identified the set of novel and informative SSR markers suitable for the study of genetic diversity in Agriophyllum

Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of ‘Pamyati Azieva × Paragon’

Leaf rust (LR) and stem rust (SR) are harmful fungal diseases of bread wheat (Triticum aestivum L.). The purpose of this study was to identify QTLs for resistance to LR and SR that are effective in two wheat-growing regions of Kazakhstan. To accomplish this task, a population of recombinant inbred lines (RILs) of ‘Pamyati Azieva × Paragon’ was grown in the northern and southeastern parts of Kazakhstan, phenotyped for LR/SR severities, and analyzed for key yield components. The study revealed a negative correlation between disease severity and plant productivity in both areas. The mapping population was genotyped using a 20,000 Illumina SNP array. A total of 4595 polymorphic SNP markers were further selected for linkage analysis after filtering based on missing data percentage and segregation distortion. Windows QTL Cartographer was applied to identify QTLs associated with LR and SR resistances in the RIL mapping population studied. Two QTLs for LR resistance and eight for SR resistance were found in the north, and the genetic positions of eight of them have matched the positions of the known Lr and Sr genes, while two QTLs for SR were novel. In the southeast, eight QTLs for LR and one for SR were identified in total. The study is an initial step of the genetic mapping of LR and SR resistance loci of bread wheat in Kazakhstan. Field trials in two areas of the country and the genotyping of the selected mapping population have allowed identification of key QTLs that will be effective in regional breeding projects for better bread wheat productivity

Morphological description and DNA barcoding study of sand rice (Agriophyllum squarrosum, Chenopodiaceae) collected in Kazakhstan

Abstract Background Sand rice (Agriophyllum squarrosum (L.) Moq.) is an annual shrub-like plant adapted to the mobile sand dunes in desert and semi-desert regions of Asia. It has a balanced nutrient composition with relatively high concentration of lipids and proteins, which results in its nutrition being similar to legumes. Sand rice’s proteins contain the full range of essential amino acids. However, calories content is more similar to wheat. These features together with desert stress resistance make sand rice a potential food crop resilient to ongoing climate change. It is also an important fodder crop (on young stages of growth) for cattle in arid regions of Kazakhstan. In our work, sand rice samples were collected from two distant regions of Kazakhstan as a part of the nation-wide project to determine genetic variation of the native flora. Results Samples were collected in western and southeastern parts of Kazakhstan separated by distances of up to 1300 km. Sequences of the nuclear ribosomal DNA ITS1-5.8S-ITS2 region and the chloroplast matK gene confirmed the identity of species defined by morphological traits. Comparison with GenBank sequences revealed polymorphic sequence positions among Kazakh populations and GenBank references, and suggested a distinction among local populations of sand rice. The phylogenetic analysis of nucleotide sequences showed a clear partition of A. squarrosum (L.) Moq. from Agriophyllum minus Fisch. & C.A. Mey, which grows in the same sand dunes environment. Conclusions DNA barcoding analyses of ITS and matK sequences showed a segregation of A. squarrosum from A. minus into separate clades in Maximum-Likelhood dendrograms. ITS analysis can be successfully used to characterize A. squarrosum populations growing quite distant from each other. The data obtained in this work provide the basis for further investigations on A. squarrosum population structure and may play a role in the screening of sand rice plants growing in desert and semi-desert environments of Central Asia and China

Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan

Barley (Hordeum vulgare L.) is one of the most produced cereal crops in the world. It has traditionally been used for the production of animal feed and for malting, as well as for human consumption. However, its production is highly affected by biotic stress factors, particularly the fungal pathogen Blumeria graminis (DC.) f. sp. hordei (Bgh), which causes powdery mildew (PM). In this study, a collection of 406 barley accessions from the USA, Kazakhstan, Europe, and Africa were assessed for resistance to PM over a 3-year period in southeastern Kazakhstan. The collection was grown in the field in 2020, 2021, and 2022 and was genotyped using the 9K SNP Illumina chip. A genome-wide association study (GWAS) was conducted to identify the quantitative trait loci (QTLs) associated with PM resistance. As a result, seven QTLs for PM resistance were detected on chromosomes 4H, 5H, and 7H (FDR p-values < 0.05). Genetic positions of two QTLs were similar to those of PM resistance QTLs previously reported in the scientific literature, suggesting that the five remaining QTLs are novel putative genetic factors for the studied trait. Haplotype analysis for seven QTLs revealed three haplotypes which were associated with total PM resistance and one haplotype associated with the high PM severity in the barley collection. Identified QTLs and haplotypes associated with the PM resistance of barley may be used for further analysis, trait pyramiding, and marker-assisted selection